This paper is a nice cautionary tale. R1a is very common in eastern Europe and less so in the Near East. Ashkenazi Jews lived in Eastern Europe, and one group of them (Levites) had high frequency of R1a than the rest. It seemed that an eastern European patrilineage had inserted itself into the Ashkenazi Levite gene pool.
It turns out that this is not the case. The specific clade R-M582 to which Ashkenazi Levites (and other non-Levites) belong to is absent in eastern Europeans and present in non-Jewish Near Easterners, making it more likely that Jews did not pick it up from eastern Europeans, but rather from some Near Eastern population. A look at the table of frequencies suggests to me an Iranic source, but I doubt that modern populations will ever allow a full resolution of such questions.
Nature Communications 4, Article number: 2928 doi:10.1038/ncomms3928
Phylogenetic applications of whole Y-chromosome sequences and the Near Eastern origin of Ashkenazi Levites
Siiri Rootsi et al.
Previous Y-chromosome studies have demonstrated that Ashkenazi Levites, members of a paternally inherited Jewish priestly caste, display a distinctive founder event within R1a, the most prevalent Y-chromosome haplogroup in Eastern Europe. Here we report the analysis of 16 whole R1 sequences and show that a set of 19 unique nucleotide substitutions defines the Ashkenazi R1a lineage. While our survey of one of these, M582, in 2,834 R1a samples reveals its absence in 922 Eastern Europeans, we show it is present in all sampled R1a Ashkenazi Levites, as well as in 33.8% of other R1a Ashkenazi Jewish males and 5.9% of 303 R1a Near Eastern males, where it shows considerably higher diversity. Moreover, the M582 lineage also occurs at low frequencies in non-Ashkenazi Jewish populations. In contrast to the previously suggested Eastern European origin for Ashkenazi Levites, the current data are indicative of a geographic source of the Levite founder lineage in the Near East and its likely presence among pre-Diaspora Hebrews.